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Artificial allosteric protein switches with machine-learning-designed receptors.

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Machine learning created minimal protein domains that act as efficient allosteric switches for biosensors. These synthetic switches enable logic gates and bioelectronic devices, showcasing advances in synthetic biology.

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Area of Science:

  • Synthetic biology
  • Biotechnology
  • Protein engineering

Background:

  • Protein allostery is crucial for biological information and energy processing.
  • Developing artificial allosteric proteins is a major goal in synthetic biology and biotechnology.

Purpose of the Study:

  • To engineer minimal ligand-binding domains as efficient receptors for single-component allosteric switches.
  • To create synthetic allosteric switches for biosensing and logic gate applications.
  • To demonstrate the practical utility of these synthetic switches in engineered cells and bioelectronic devices.

Main Methods:

  • Machine learning for engineering minimal ligand-binding domains.
  • Construction of colorimetric, luminescent, and electrochemical biosensors.
  • Compilation of biosensors into intramolecular YES and AND logic gates.
  • Hydrogen/deuterium exchange mass spectrometry and 19F nuclear magnetic resonance analyses.
  • Engineering Escherichia coli for steroid-dependent antibiotic resistance.
  • Development of bioelectronic devices for steroid hormone quantification.

Main Results:

  • Machine-learning-engineered minimal domains function as efficient receptors in allosteric switches without global conformational change.
  • Synthetic allosteric switches were successfully compiled into intramolecular YES and AND logic gates.
  • Ligand binding was shown to reduce conformational entropy, enhancing reporter domain catalytic activity.
  • Demonstrated utility through engineered E. coli with steroid-dependent antibiotic resistance.
  • Developed bioelectronic devices capable of quantifying steroid hormones.

Conclusions:

  • Minimal engineered domains can serve as effective receptors in synthetic allosteric switches.
  • These synthetic switches offer versatile platforms for biosensing, logic operations, and bioelectronic applications.
  • The approach holds significant potential for advancing synthetic biology and biotechnology tools.